| Summary: | Coral reefs worldwide are being threatened by increasing seawater temperatures, ocean acidification, overfishing, pollution, and increased intensity of storms. Small scale spatial (< 1 km) variability in temperature has been observed on coral reefs; however, it currently cannot be measured by remote sensing products. Furthermore, small scale temporal (< 1 cycle/day) variability has been shown to be significant for coral bleaching resilience. Here, I aim to further our understanding of the physical processes which drive the spatial and temporal variability in environmental parameters on reef ecosystems. First, I examine the physical processes driving flow on the east reef flat at Dongsha Atoll, in the northern South China Sea. There are observable thermal microclimates on the shallow and wide reef flat, which distinguishes the reef from open ocean temperatures. A simple analytical model of flow reveals that tides and surface waves are driving flow here, and the influence is variable in time and space. The wide reef flat at Dongsha Atoll leads gradients in the residence time and source of water (offshore vs. lagoon), and an asymmetry in the tidal excursion of water on the reef flat. Next, I investigate the influence of the internal waves on the thermal and nutrient environment on the east reef flat at Dongsha Atoll. A heat budget was created to estimate the temperature on the reef without the internal wave influence, and instantaneous temperatures on the reef can be up to 2.0°C warmer. Also, internal waves increase the instantaneous flux of nutrients onshore by four-fold, which can have significantly influence biogeochemistry on the reef. Finally, high spatial and temporal resolution temperature measurements were collected from three coral reefs with different morphologies, and used to determine the physical processes driving reef scale variability in water temperature. Distinctive thermal environments were observed, including reef-scale gradients in mean temperature and daily temperature range (DTR), which distinguish the shallow reefs from offshore. Daily temperature range has been shown to be the most influential metric in predicting bleaching prevalence on reefs, and studies have shown it can be predicted from average water depth. By using a heat budget, and including advection in the estimate of temperature, we are able improve predictions of DTR with minimal in-situ measurements.
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